› 8jvd

X-ray diffraction
1.7Å resolution

Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening

Released:
DOI: 10.2210/pdb8jvd/pdb
PDB entry 8jvd coloured by chain, front view.
PDB entry 8jvd coloured by chain, side view.
PDB entry 8jvd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening.
Loh YY, Anantharajan J, Huang Q, Xu W, Fulwood J, Ng HQ, Ng EY, Gea CY, Choong ML, Tan QW, Koh X, Lim WH, Nacro K, Cherian J, Baburajendran N, Ke Z, Kang C
Protein Sci 33 e4904 (2024)
PMID: 38358126

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192476 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin-conjugating enzyme E2 T Chain: A
Molecule details ›
Chain: A
Length: 156 amino acids
Theoretical weight: 17.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NPD8 (Residues: 1-154; Coverage: 78%)
Gene names: HSPC150, PIG50, UBE2T
Sequence domains: Ubiquitin-conjugating enzyme

Ligands and Environments

1 bound ligand:
Ligand V2R 1 x V2R
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P43212
Unit cell:
a: 54.636Å b: 54.636Å c: 182.728Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.228 0.255
Expression system: Escherichia coli

Quick links